Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity

The archaeal/eukaryotic proliferating cell nuclear antigen (PCNA) toroidal clamp interacts with a host of DNA modifying enzymes, providing a stable anchorage and enhancing their respective processivities. Given the broad range of enzymes with which PCNA has been shown to interact, relatively little is known about the mode of assembly of functionally meaningful combinations of enzymes on the PCNA clamp. We have determined the X-ray crystal structure of the Sulfolobus solfataricus PCNA1–PCNA2 heterodimer, bound to a single copy of the flap endonuclease FEN1 at 2.9 Å resolution. We demonstrate the specificity of interaction of the PCNA subunits to form the PCNA1–PCNA2–PCNA3 heterotrimer, as well as providing a rationale for the specific interaction of the C-terminal PIP-box motif of FEN1 for the PCNA1 subunit. The structure explains the specificity of the individual archaeal PCNA subunits for selected repair enzyme ‘clients’, and provides insights into the co-ordinated assembly of sequential enzymatic steps in PCNA-scaffolded DNA repair cascades.     

XRCC1 co-localizes and physically interacts with PCNA

X-ray Repair Cross Complementing 1 (XRCC1) is thought to function as a scaffolding protein in both base excision repair and single-strand break repair (SSBR), since it interacts with several proteins participating in these related pathways and has no known enzymatic activity. Moreover, studies indicate that XRCC1 possesses discrete G₁ and S phase-specific functions. To further define the contribution of XRCC1 to DNA metabolism, we determined the in vivo localization pattern of this protein and searched for novel protein interactors. We report here that XRCC1 co-localizes with proliferating cell nuclear antigen (PCNA) at DNA replication foci, observed exclusively in the S phase of undamaged HeLa cells. Furthermore, fluorescence resonance energy transfer (FRET) analysis and co-immunoprecipitation indicate that XRCC1 and PCNA are in a complex and likely physically interact in vivo. In vitro biochemical analysis demonstrated that these two proteins associate directly, with the interaction being mediated by residues between amino acids 166 and 310 of XRCC1. The current evidence suggests a model where XRCC1 is sequestered via its interaction with PCNA to sites of DNA replication factories to facilitate efficient SSBR in S phase.     

HUWE1 interacts with PCNA to alleviate replication stress

Defects in DNA replication, DNA damage response, and DNA repair compromise genomic stability and promote cancer development. In particular, unrepaired DNA lesions can arrest the progression of the DNA replication machinery during S‐phase, causing replication stress, mutations, and DNA breaks. HUWE1 is a HECT‐type ubiquitin ligase that targets proteins involved in cell fate, survival, and differentiation. Here, we report that HUWE1 is essential for genomic stability, by promoting replication of damaged DNA. We show that HUWE1‐knockout cells are unable to mitigate replication stress, resulting in replication defects and DNA breakage. Importantly, we find that this novel role of HUWE1 requires its interaction with the replication factor PCNA, a master regulator of replication fork restart, at stalled replication forks. Finally, we provide evidence that HUWE1 mono‐ubiquitinates H2AX to promote signaling at stalled forks. Altogether, our work identifies HUWE1 as a novel regulator of the replication stress response.     

PCNA promotes processive DNA end resection by Exo1

Exo1-mediated resection of DNA double-strand break ends generates 3′ single-stranded DNA overhangs required for homology-based DNA repair and activation of the ATR-dependent checkpoint. Despite its critical importance in inducing the overall DNA damage response, the mechanisms and regulation of the Exo1 resection pathway remain incompletely understood. Here, we identify the ring-shaped DNA clamp PCNA as a new factor in the Exo1 resection pathway. Using mammalian cells, Xenopus nuclear extracts and purified proteins, we show that after DNA damage, PCNA loads onto double-strand breaks and promotes Exo1 damage association through direct interaction with Exo1. By tethering Exo1 to the DNA substrate, PCNA confers processivity to Exo1 in resection. This role of PCNA in DNA resection is analogous to its function in DNA replication where PCNA serves as a processivity co-factor for DNA polymerases.     

Similarities and differences between Arabidopsis PCNA1 and PCNA2 in complementing the yeast DNA damage tolerance defect

Proliferating cell nuclear antigen (PCNA) forms a homotrimer that functions as a sliding clamp essential for genomic DNA replication. It is also directly involved in the regulation of cellular response to DNA damage, which is typically achieved through its covalent modifications. The Arabidopsis genome encodes two PCNAs with only nine amino acid variations, yet two recent reports indicate that AtPCNA2 plays a more critical role in DNA damage response than AtPCNA1. In this study, it was found that both AtPCNAs were able to functionally complement the essential roles of yeast POL30 (PCNA), but failed to rescue the DNA damage tolerance defect of pol30. Surprisingly, the AtPCNA1-K164R mutation rendered cells more tolerant to DNA damage, which appears to be dependent on PCNA sumoylation but not ubiquitination. Two critical residues proximal in structure to K164 were identified in AtPCNAs that contribute to their differences in DNA damage tolerance, since their amino acid substitutions alter the level of DNA damage tolerance. Collectively, it is concluded that the two AtPCNAs differ in their efficiency for ubiquitination and sumoylation, leading to their differential responses to DNA damage in yeast cells.     

Two modes of FEN1 binding to PCNA regulated by DNA

The FEN1 nuclease functions during Okazaki fragment maturation in the eukaryotic cell. Like many other proliferating cell nuclear antigen (PCNA)-binding proteins, FEN1 interacts with the interdomain connector loop (IDCL) of PCNA, and PCNA greatly stimulates FEN1 activity. A yeast IDCL mutant pcna-79 (IL126,128AA) failed to interact with FEN-1, but, surprisingly, pcna-79 was still very active in stimulating FEN1 activity. In contrast, a C-terminal mutant pcna-90 (PK252,253AA) showed wild-type binding to FEN1 in solution, but poorly stimulated FEN1 activity. When PCNA was loaded onto a DNA substrate coupled to magnetic beads, it stabilized retention of FEN1 on the DNA. In this DNA-dependent binding assay, pcna-79 also stabilized retention of FEN1, but pcna-90 was inactive. Therefore, in the absence of DNA, FEN1 interacts with PCNA mainly through the IDCL. However, when PCNA encircles the DNA, the C-terminal domain of PCNA rather than its IDCL is important for binding FEN1. An FF-->GA mutation in the PCNA-interaction domain of FEN1 severely decreased both modes of interaction with PCNA and resulted in replication and repair defects in vivo.     

Cytoskeleton integrity influences XRCC1 and PCNA dynamics at DNA damage

On induction of DNA damage with 405-nm laser light, proteins involved in base excision repair (BER) are recruited to DNA lesions. We find that the dynamics of factors typical of either short-patch (XRCC1) or long-patch (PCNA) BER are altered by chemicals that perturb actin or tubulin polymerization in human cells. Whereas the destabilization of actin filaments by latrunculin B, cytochalasin B, or Jasplakinolide decreases BER factor accumulation at laser-induced damage, inhibition of tubulin polymerization by nocodazole increases it. We detect no recruitment of actin to sites of laser-induced DNA damage, yet the depolymerization of cytoplasmic actin filaments elevates both actin and tubulin signals in the nucleus. While published evidence suggested a positive role for F-actin in double-strand break repair in mammals, the enrichment of actin in budding yeast nuclei interferes with BER, augmenting sensitivity to Zeocin. Our quantitative imaging results suggest that the depolymerization of cytoplasmic actin may compromise BER efficiency in mammals not only due to elevated levels of nuclear actin but also of tubulin, linking cytoskeletal integrity to BER.     

Structural basis for recruitment of human flap endonuclease 1 to PCNA

Flap endonuclease-1 (FEN1) is a key enzyme for maintaining genomic stability and replication. Proliferating cell nuclear antigen (PCNA) binds FEN1 and stimulates its endonuclease activity. The structural basis of the FEN1-PCNA interaction was revealed by the crystal structure of the complex between human FEN1 and PCNA. The main interface involves the C-terminal tail of FEN1, which forms two beta-strands connected by a short helix, the betaA-alphaA-betaB motif, participating in beta-beta and hydrophobic interactions with PCNA. These interactions are similar to those previously observed for the p21CIP1/WAF1 peptide. However, this structure involving the full-length enzyme has revealed additional interfaces that are involved in the core domain. The interactions at the interfaces maintain the enzyme in an inactive 'locked-down' orientation and might be utilized in rapid DNA-tracking by preserving the central hole of PCNA for sliding along the DNA. A hinge region present between the core domain and the C-terminal tail of FEN1 would play a role in switching the FEN1 orientation from an inactive to an active orientation.     

Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates

Flap endonuclease 1 (Fen1) is a highly conserved structure-specific nuclease that catalyses a specific incision to remove 5′ flaps in double-stranded DNA substrates. Fen1 plays an essential role in key cellular processes, such as DNA replication and repair, and mutations that compromise Fen1 expression levels or activity have severe health implications in humans. The nuclease activity of Fen1 and other FEN family members can be stimulated by processivity clamps such as proliferating cell nuclear antigen (PCNA); however, the exact mechanism of PCNA activation is currently unknown. Here, we have used a combination of ensemble and single-molecule Förster resonance energy transfer together with protein-induced fluorescence enhancement to uncouple and investigate the substrate recognition and catalytic steps of Fen1 and Fen1/PCNA complexes. We propose a model in which upon Fen1 binding, a highly dynamic substrate is bent and locked into an open flap conformation where specific Fen1/DNA interactions can be established. PCNA enhances Fen1 recognition of the DNA substrate by further promoting the open flap conformation in a step that may involve facilitated threading of the 5′ ssDNA flap. Merging our data with existing crystallographic and molecular dynamics simulations we provide a solution-based model for the Fen1/PCNA/DNA ternary complex.     

PCNA dependent cellular activities tolerate dramatic perturbations in PCNA client interactions

Proliferating cell nuclear antigen (PCNA) is an essential cofactor for DNA replication and repair, recruiting multiple proteins to their sites of action. We examined the effects of the PCNA^S228I mutation that causes PCNA-associated DNA repair disorder (PARD). Cells from individuals affected by PARD are sensitive to the PCNA inhibitors T3 and T2AA, showing that the S228I mutation has consequences for undamaged cells. Analysis of the binding between PCNA and PCNA-interacting proteins (PIPs) shows that the S228I change dramatically impairs the majority of these interactions, including that of Cdt1, DNMT1, PolD3^p66 and PolD4^p12. In contrast p21 largely retains the ability to bind PCNA^S228I. This property is conferred by the p21 PIP box sequence itself, which is both necessary and sufficient for PCNA^S228I binding. Ubiquitination of PCNA is unaffected by the S228I change, which indirectly alters the structure of the inter-domain connecting loop. Despite the dramatic in vitro effects of the PARD mutation on PIP-degron binding, there are only minor alterations to the stability of p21 and Cdt1 in cells from affected individuals. Overall our data suggests that reduced affinity of PCNA^S228I for specific clients causes subtle cellular defects in undamaged cells which likely contribute to the etiology of PARD.     

Structure of monoubiquitinated PCNA

Ubiquitination of proliferating cell nuclear antigen (PCNA) to ub-PCNA is essential for DNA replication across bulky template lesions caused by UV radiation and alkylating agents, as ub-PCNA orchestrates the recruitment and switching of translesion synthesis (TLS) polymerases with replication polymerases. This allows replication to proceed, leaving the DNA to be repaired subsequently. Defects in a TLS polymerase, Pol η, lead to a form of Xeroderma pigmentosum, a disease characterized by severe skin sensitivity to sunlight damage and an increased incidence of skin cancer. Structurally, however, information on how ub-PCNA orchestrates the switching of these two classes of polymerases is lacking. We have solved the structure of ub-PCNA and demonstrate that the ubiquitin molecules in ub-PCNA are radially extended away from the PCNA without structural contact aside from the isopeptide bond linkage. This unique orientation provides an open platform for the recruitment of TLS polymerases through ubiquitin-interacting domains. However, the ubiquitin moieties, to the side of the equatorial PCNA plane, can place spatial constraints on the conformational flexibility of proteins bound to ub-PCNA. We show that ub-PCNA is impaired in its ability to support the coordinated actions of Fen1 and Pol δ in assays mimicking Okazaki fragment processing. This provides evidence for the novel concept that ub-PCNA may modulate additional DNA transactions other than TLS polymerase recruitment and switching.     

Damage-specific modification of PCNA

Okazaki fragment processing is an integral part of DNA replication. For a long time, we assumed that the maturation of these small RNA-primed DNA fragments did not necessarily have to occur during S phase, but could be postponed to late in S phase after the bulk of DNA synthesis had been completed. This view was primarily based on the arrest phenotype of temperature-sensitive DNA ligase I mutants in yeast, which accumulated with an almost fully duplicated set of chromosomes. However, many temperature-sensitive alleles can be leaky, and the re-evaluation of DNA ligase I-deficient cells has offered new and unexpected insights into how cells keep track of lagging strand synthesis. It turns out that if Okazaki fragment joining goes awry, cells have their own alarm system in the form of ubiquitin that is conjugated to the replication clamp PCNA. Although this modification results in mono- and poly-ubiquitination of PCNA, it is genetically distinct from the known post-replicative repair mark at lysine 164. In this Extra View, we discuss the possibility that eukaryotic cells utilize different enzymatic pathways and ubiquitin attachment sites on PCNA to alert the replication machinery to the accumulation of single-stranded gaps or nicks behind the fork.     

Readers of PCNA modifications

The eukaryotic sliding clamp, proliferating cell nuclear antigen (PCNA), acts as a central coordinator of DNA transactions by providing a multivalent interaction surface for factors involved in DNA replication, repair, chromatin dynamics and cell cycle regulation. Posttranslational modifications (PTMs), such as mono- and polyubiquitylation, sumoylation, phosphorylation and acetylation, further expand the repertoire of PCNA’s binding partners. These modifications affect PCNA’s activity in the bypass of lesions during DNA replication, the regulation of alternative damage processing pathways such as homologous recombination and DNA interstrand cross-link repair, or impact on the stability of PCNA itself. In this review, we summarise our current knowledge about how the PTMs are “read” by downstream effector proteins that mediate the appropriate action. Given the variety of interaction partners responding to PCNA’s modified forms, the ensemble of PCNA modifications serves as an instructive model for the study of biological signalling through PTMs in general.     

HDM2 ERKs PCNA

In this issue, a study by Groehler and Lannigan (2010. J. Cell Biol. doi:10.1083/jcb.201002124) sheds light on the regulation of proliferating cell nuclear antigen (PCNA) turnover and how it is counteracted by the small chromatin-bound kinase ERK8 (extracellular signal-regulated kinase 8). Importantly, inactivation of ERK8 results in genome instability and is associated with cell transformation.Almost 30 yr ago, proliferating cell nuclear antigen (PCNA) was first identified in dividing cells using sera derived from patients suffering from systemic lupus erythematosus (Takasaki et al., 1981). A few years later, the “mother” of all cancer markers had been associated with DNA synthesis (Madsen and Celis, 1985), but it wasn’t until 1988 that Bauer and Burgers (1988) and Prelich and Stillman (1988) discovered that the homotrimeric clamp served as a processivity factor for DNA polymerases. In 1992, Shivji et al. (1992) showed that PCNA was required for DNA repair, and 10 yr later, it was identified as a target of ubiquitin and SUMO (small ubiquitin-like modifier) conjugation after exposure to ultraviolet light (Hoege et al., 2002). For a protein that has been in the spotlight of modern biochemistry, it is quite remarkable that almost nothing is known about its normal cellular turnover.Insight into this process comes now from the study of an unlikely regulator. In this issue, Groehler and Lannigan (2010) demonstrate that the relatively poorly characterized ERK8 (extracellular signal-regulated kinase 8) takes center stage in the regulation of PCNA stability in primary mammary epithelial cells. The ERK family of kinases belongs to the mitogen-activated protein kinase superfamily and carries a Thr-Glu-Tyr (T-E-Y) activation motif that needs to be phosphorylated to enable kinase activity (Abe et al., 2002). Interestingly, ERK8 also needs to bind to chromatin to become active. The authors identified a highly conserved PXXXP motif in the C-terminal half of ERK8 that appeared to confer autoinhibition, an activity which is relieved upon chromatin binding. Relatively close by, in the middle of ERK8, resides a PCNA-interacting peptide (PIP) box required for the interaction with PCNA (Warbrick, 1998). Curiously, only the chromatin-bound fraction of ERK8 bound to the chromatin-bound fraction of PCNA. However, a functional PIP box was not required for ERK8 to associate with nuclear DNA in the cell. These results argue that ERK8 is not anchored to chromatin by PCNA but associates with it independently. Moreover, they strongly suggest that ERK8’s PIP box binds to PCNA only when the kinase is associated with chromatin. Importantly, overexpression of an ERK8 PIP box mutant resulted in destabilization of PCNA. The effect on PCNA stability seemed to be highly specific, as depletion of ERK8 caused codepletion of PCNA but did not lead to a decrease in steady-state levels of a variety of other cell cycle regulators.Why is the interaction with PCNA confined to chromatin? The reason is likely due to the fact that ERK8’s PIP box is buried in the middle of the protein. Most PCNA-interacting proteins carry their PIP box either at the N or C terminus (Vivona and Kelman, 2003). One other well-studied example for a protein with an internal PIP box is the essential replication factor MCM10 (minichromosome maintenance protein 10). MCM10 undergoes cell cycle–regulated modification, which probably induces a conformational switch that is necessary for the PIP box–mediated interaction with PCNA (Das-Bradoo et al., 2006). In the same vein, it is conceivable that chromatin association and the accompanying relief of autoinhibition of ERK8 cause the middle portion of the kinase to change its configuration, thereby assuming a functional PIP box domain that can be recognized by PCNA. In situations in which the rapid unloading of PCNA is required, regulation of ERK8 may be the most effective way to dispose of chromatin-bound PCNA, which is known to have an exceedingly low exchange rate (Sporbert et al., 2002). Despite the fact that interaction with ERK8 is necessary to stabilize chromatin-bound PCNA, it remains unclear whether PCNA is a direct target of ERK8-mediated phosphorylation.The next goal of Groehler and Lannigan (2010) was to dissect the mechanism underlying the ERK8-regulated degradation of PCNA. Based on the consideration that physical contact between the kinase and PCNA was an integral part of the protection, they hypothesized that ERK8 might compete with an E3 ubiquitin ligase that may target PCNA via its own PIP box. This turned out to be a smart guess because the only candidate to test was the E3 ligase HDM2, the human homologue of murine double minute 2 (Momand et al., 1992). In a set of well-controlled experiments, the authors not only demonstrate that HDM2 interacts directly with and degrades PCNA when ERK8 is absent, but they also exclude indirect effects by p53 and retinoblastoma (Rb) on this process. p53 is a direct target of HDM2 and is stabilized when their interaction is inhibited (Tao and Levine, 1999). Elevated levels of p53 trigger cell cycle arrest concomitant with hypophosphorylation of Rb, but none of these changes affect the stability of PCNA. It is not hard to imagine that the loss of chromatin-bound PCNA has severe consequences for the functionality of DNA replication and repair, resulting in chromosome breakage. The authors argued that a similar level of genome instability should be visible in ERK8-depleted cells. This was indeed the case as visualized by the accumulation of γ-H2AX foci and broken DNA (Rogakou et al., 1998). Importantly, Groehler and Lannigan (2010) observed similar effects in the ERK8 PIP box mutant, further lending credence to their model. It is worthwhile pointing out that the turnover of PCNA expands the spectrum of replication factors whose degradation is tightly linked to chromatin. CDT1, a member of the prereplication complex (Cook, 2009), is rapidly degraded in the face of DNA damage. Its degradation occurs exclusively on the chromatin-associated fraction of the protein pool and is dependent on CDT1 binding to PCNA (Arias and Walter, 2005; Hu and Xiong, 2006; Senga et al., 2006).An important question that this study raises is of course to what extent, if at all, is PCNA turnover deregulated in cancer cells? The commonly high levels of PCNA in transformed cells would be most compatible with a deregulation of ERK8 and/or HDM2 to provide a significant growth advantage. Indeed, the authors show in the last part of their study that in at least two transformed cell lines, PCNA is rendered inert to the presence of ERK8. They speculate that the underlying reason is a defect in HDM2, and although this is the most likely explanation, it still needs to be validated. It will be interesting to see how common the misregulation of PCNA turnover is in cancer tissues. At this point, it is intriguing to envision a dynamic scenario in which a two-step mechanism facilitates cell transformation (Fig. 1). Initially, deregulation of ERK8 may cause PCNA levels to decrease. This would contribute to genome instability and the accumulation of new mutations, including those affecting proper function of HDM2. In step two, deregulation of HDM2 may turn things around and result in an increase of PCNA, supporting rapid proliferation.Open in a separate windowFigure 1.Role of ERK8 in maintaining genome stability. (A) In normal cells, chromatin-bound ERK8 interacts with the chromatin fraction of PCNA, which resides at the replication fork (here just shown at the leading strand for simplicity). ERK8 binding inhibits the E3 ubiquitin ligase HDM2 from interacting with PCNA. (B) In cancer cells, inactivation of ERK8 enables HDM2 to interact with and ubiquitinate PCNA, targeting it for degradation. A decrease in PCNA levels causes an increase in DNA damage, resulting in the accumulation of new mutations. These new mutations may render HDM2 nonfunctional (rectangular form), which ultimately results in an increase of PCNA stability and facilitates cell proliferation. The homotrimeric PCNA structure (Protein Data Bank ID 2OD8) was generated using the Chimera software program (Pettersen et al., 2004).     

Damage-specific modification of PCNA

Okazaki fragment processing is an integral part of DNA replication. For a long time, we assumed that the maturation of these small RNA-primed DNA fragments did not necessarily have to occur during S phase, but could be postponed to late in S phase after the bulk of DNA synthesis had been completed. This view was primarily based on the arrest phenotype of temperature-sensitive DNA ligase I mutants in yeast, which accumulated with an almost fully duplicated set of chromosomes. However, many temperature-sensitive alleles can be leaky and the re-evaluation of DNA ligase I-deficient cells has offered new and unexpected insights into how cells keep track of lagging strand synthesis. It turns out that if Okazaki fragment joining goes awry, cells have their own alarm system in the form of ubiquitin that is conjugated to the replication clamp PCNA. Although this modification results in mono- and poly-ubiquitination of PCNA, it is genetically distinct from the known post-replicative repair mark at lysine 164. In this Extra View, we discuss the possibility that eukaryotic cells utilize different enzymatic pathways and ubiquitin attachment sites on PCNA to alert the replication machinery to the accumulation of single-stranded gaps or nicks behind the fork.Key words: DNA ligase I, DNA replication, Okazaki fragment processing, PCNA, ubiquitin, SUMO     

The archaeal PCNA proteins

PCNA (proliferating-cell nuclear antigen) is a ring-shaped protein that encircles duplex DNA and plays an essential role in many DNA metabolic processes. The PCNA protein interacts with a large number of cellular factors and modulates their enzymatic activities. In the present paper, we summarize the structures, functions and interactions of the archaeal PCNA proteins.     

Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin

Chromatin assembly factor 1 (CAF-1) is required for inheritance of epigenetically determined chromosomal states in vivo and promotes assembly of chromatin during DNA replication in vitro. Herein, we demonstrate that after DNA replication, replicated, but not unreplicated, DNA is also competent for CAF-1-dependent chromatin assembly. The proliferating cell nuclear antigen (PCNA), a DNA polymerase clamp, is a component of the replication-dependent marking of DNA for chromatin assembly. The clamp loader, replication factor C (RFC), can reverse this mark by unloading PCNA from the replicated DNA. PCNA binds directly to p150, the largest subunit of CAF-1, and the two proteins colocalize at sites of DNA replication in cells. We suggest that PCNA and CAF-1 connect DNA replication to chromatin assembly and the inheritance of epigenetic chromosome states.